GitHub - akinsse/cobratoolbox: COnstraint-Based Reconstruction and Analysis toolbox

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COnstraint-Based Reconstruction and Analysis toolbox

GPL-3.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 177 Commits
design		design
docs		docs
external		external
fluxomics		fluxomics
gapFilling		gapFilling
io		io
maps		maps
modelGeneration		modelGeneration
papers		papers
rFBA		rFBA
reconstruction		reconstruction
sampling		sampling
solvers		solvers
subspaces		subspaces
testing		testing
thermo		thermo
tools		tools
topology		topology
versions		versions
.gitignore		.gitignore
.gitmodules		.gitmodules
CHANGELOG		CHANGELOG
INSTALL.txt		INSTALL.txt
LEGAL.txt		LEGAL.txt
LICENSE.txt		LICENSE.txt
MOMA.m		MOMA.m
OMNI.m		OMNI.m
README		README
TODO		TODO
addLoopLawConstraints.m		addLoopLawConstraints.m
analyzeRxns.m		analyzeRxns.m
changeGeneAssociation.m		changeGeneAssociation.m
changeObjective.m		changeObjective.m
changeRxnBounds.m		changeRxnBounds.m
changeRxnMets.m		changeRxnMets.m
checkCobraModelUnique.m		checkCobraModelUnique.m
checkDuplicateRxn.m		checkDuplicateRxn.m
checkMassChargeBalance.m		checkMassChargeBalance.m
checkObjective.m		checkObjective.m
computeElementalMatrix.m		computeElementalMatrix.m
computeMW.m		computeMW.m
convertIrrevFluxDistribution.m		convertIrrevFluxDistribution.m
convertModelToEX.m		convertModelToEX.m
convertToIrreversible.m		convertToIrreversible.m
convertToReversible.m		convertToReversible.m
deleteModelGenes.m		deleteModelGenes.m
detectDeadEnds.m		detectDeadEnds.m
doubleGeneDeletion.m		doubleGeneDeletion.m
doubleRobustnessAnalysis.m		doubleRobustnessAnalysis.m
dynamicFBA.m		dynamicFBA.m
enumerateOptimalSolutions.m		enumerateOptimalSolutions.m
extractCompModel.m		extractCompModel.m
extractMetModel.m		extractMetModel.m
extractSubNetwork.m		extractSubNetwork.m
extractSubSysModel.m		extractSubSysModel.m
findBlockedReaction.m		findBlockedReaction.m
findEpistaticInteractions.m		findEpistaticInteractions.m
findExcRxns.m		findExcRxns.m
findGeneIDs.m		findGeneIDs.m
findGenesFromRxns.m		findGenesFromRxns.m
findMetIDs.m		findMetIDs.m
findMetabolicJunctions.m		findMetabolicJunctions.m
findNeighborRxns.m		findNeighborRxns.m
findRxnIDs.m		findRxnIDs.m
findRxnsFromGenes.m		findRxnsFromGenes.m
findRxnsFromMets.m		findRxnsFromMets.m
findSubSysGen.m		findSubSysGen.m
findTransRxns.m		findTransRxns.m
fluxVariability.m		fluxVariability.m
folders.m		folders.m
generateDoc.m		generateDoc.m
generateRules.m		generateRules.m
geometricFBA.m		geometricFBA.m
identifyCorrelSets.m		identifyCorrelSets.m
initCobraToolbox.m		initCobraToolbox.m
installSBMLToolbox.m		installSBMLToolbox.m
isSameCobraModel.m		isSameCobraModel.m
keepCompartment.m		keepCompartment.m
linearMOMA.m		linearMOMA.m
moveRxn.m		moveRxn.m
optimizeCbModel.m		optimizeCbModel.m
optimizeCbModelNLP.m		optimizeCbModelNLP.m
optimizeTwoCbModels.m		optimizeTwoCbModels.m
pFBA.m		pFBA.m
parseMetNames.m		parseMetNames.m
parseRxnFormula.m		parseRxnFormula.m
phenotypePhasePlane.m		phenotypePhasePlane.m
printConstraints.m		printConstraints.m
printFluxVector.m		printFluxVector.m
printRxnFormula.m		printRxnFormula.m
printUptakeBound.m		printUptakeBound.m
productionEnvelope.m		productionEnvelope.m
randomObjFBASol.m		randomObjFBASol.m
reassignFwBwMatch.m		reassignFwBwMatch.m
reduceModel.m		reduceModel.m
removeDeadEnds.m		removeDeadEnds.m
robustnessAnalysis.m		robustnessAnalysis.m
scaleSMatrix.m		scaleSMatrix.m
singleGeneDeletion.m		singleGeneDeletion.m
singleRxnDeletion.m		singleRxnDeletion.m

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For convenience, we provide the SBMLToolbox 4.1.0, and glpk_mex in external/toolboxes for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit).  If you do not wish to use these items please delete the directories.  If you require these external libraries for other architectures please ask google or visit their respective websites.

To read / write SBML files you must install libSBML 5.5.0 from here: http://sourceforge.net/projects/sbml/files/libsbml/

From MATLAB, run
  initCobraToolbox


NOTE: If you do not have gurobi_mex and tomlab installed on your machine, you will get some warnings and some errors.  The COBRA Toolbox will try to use glpk if it cannot find gurobi for LP / MILP.  To solve any NLP problems you need tomlab_snopt.

After running initCobraToolbox, run
  testAll
to see what functions will work with your current configuration.  Note, it is likely that one or more functions will not work unless you have  tomlab with snopt installed.